PHILADELPHIA  In the offseason, the Padres signed a setup man for $15.5 million. Joaquin Benoit joined closer Huston Street in a fortified bullpen, on a team with a franchise-record payroll. Together, Benoit and Street account for nearly 15 percent of the pie.

So far this season, the Padres have trailed after six innings in 36 of their 66 games. They went into the seventh inning of Thursday’s finale at Citizens Bank Park with a two-run deficit. They emerged with a 7-3 loss, muddied by a constant rain, swept by the Phillies, a team in last place.

There, the Padres found themselves Thursday afternoon, having displaced the Diamondbacks in the National League West’s cellar. For the first time this year, they are 10 games under .500. Too often, Street and Benoit can only watch. Between the two of them, only Benoit pitched in the three-game series, logging one scoreless inning.

The Padres are now 3-33 when trailing after six innings. It was a scenario they seemed poised to avoid, only to be stung for the second consecutive day by Philadelphia’s Reid Brignac. Brignac, who had delivered the walk-off home run in Wednesday’s game, came to the plate in the bottom of the sixth, this time as a pinch-hitter. The score was tied, 2-2. This time, Brignac lashed an opposite-field double off Dale Thayer, scoring a pair of runs and dealing the Padres grim comeback odds.

They grew virtually nonexistent in the seventh, when John Mayberry parked a three-run homer in the left-field seats. It was the first home run allowed this season by Alex Torres, another new addition to the Padres’ bullpen.

The Padres allowed themselves to be put in this position. They took a 2-0 lead in the first against Phillies starter Kyle Kendrick. Will Venable and Everth Cabrera opened with consecutive singles. Chase Headley drove in Venable with a double, another run scoring because of a fielding error.

Over the next five innings, Kendrick scattered four hits.

“He got his change-up working as the game went on,” Padres manager Bud Black said. “He spotted the fastball a little bit better than he did the first couple hitters. For lack of a better term, he kept us off balance.”

Coming off a career-worst start, Eric Stults went five innings for the Padres, allowing eight hits and a walks.

“He hung in there on three days’ rest,” Padres manager Bud Black said. “He gave us an opportunity in the middle part of the game to flip the momentum to our side.”

It was an opportunity unseized. The Phillies pounced in the sixth. For the third time on the afternoon, Stults allowed back-to-back hits to begin an inning. He was relieved by Thayer, who recorded an out before winning a 13-pitch battle with Ryan Howard. Brignac strode to the plate.

The left-handed hitter saw just four pitches, the last a fastball on the outer half of the plate. He socked it to left-center and cruised into second as the crowd roared.

“We were just looking to go outside,” Padres catcher Yasmani Grandal said. “The past couple days, (Brignac’s) been looking for something out in front to drive, to pull, and he showed it (Wednesday). He made a good adjustment. We made a good pitch, and that’s the thing about baseball. You can make the best pitch in the world and still have a negative outcome.”

Grandal launched his sixth home run of the season in the top of the ninth, though the game would remain out of reach. It was Grandal’s first extra-base hit since May 23, when he also homered. This one came against flame-throwing reliever Ken Giles, who was making his big-league debut.